South African Medical Research Council (SAMRC)Wastewater surveillance of SARS-CoV-2 RNA in South Africa

Scientific trends have revealed that the collection and analysis of data on the occurrence and fate of non-infectious SARS-CoV-2 RNA in wastewater provide the basis for a surveillance system to track the circulation of COVID-19 in communities. An effective wastewater-based epidemiology (WBE) system is critical in South Africa where health systems infrastructure, testing systems, personal protective equipment (PPE) and human resource capacity are limited.

Wastewater surveillance of SARS-CoV-2 RNA in South Africa

Driven by the urgent need to support the national effort to combat COVID-19 in South Africa, a collective of five SAMRC Research Units (the Environment & Health Research Unit, the Biomedical Research Innovation Platform, the Biostatistics Research Unit, the Genomics Centre and the Tuberculosis Platform) established wastewater-based epidemiology as a recognized method to detect the emergence and spread of local COVID-19 infections in South Africa. This work has culminated in the formal recognition of the SAMRC Wastewater Surveillance and Research Programme (WSARP). Our weekly wastewater surveillance programme oversees the collection of samples from 72 sites every Monday. The samples are then analyzed by one of our 5 partner laboratories across 4 provinces. The sites represent both urban (metro) and peri-urban (district) catchments serving ±7.5 million inhabitants. The results are released to all local authorities within a target period of 48 hours and in key settings provided directly to strategic teams to inform decision-making to combat the disease. In addition to these weekly reports, a dashboard was established to share results with the general public and the broader public health community.

The WSARP has leveraged funding from the South African Medical Research Council (SAMRC), Michael and Susan Dell Foundation, Solidarity Fund, UK Research and Innovation and the Department of Science and Innovation.

“Through partnerships and support from multiple funders, the SAMRC WSARP has laid the foundation for wastewater surveillance systems to track COVID-19,” said Dr Renée Street.

In early 2022, WSARP will expand to a further two provinces, namely KwaZulu-Natal and Free State. With capacity development being a key component of WSARP, partnerships were established with under-resourced institutions so that staff and students receive training in methods for SARS CoV-2 RNA detection in wastewater. Mentoring networks across universities support numerous students through WSARP.

WSARP has also been key in tracking variants of concern.

“We have trained our partner universities on variant testing using a rapid PCR method. It has been useful to track the geographical spread of the different variants” said Prof Rabia Johnson.

Furthermore, the SAMRC genomics centres undertake next-generation sequencing to screen for unknown variants.

“WSARP has played an important role in informing stakeholders’ decision-making around COVID-19 at national and local levels in South Africa. Of equal relevance is that we have built a platform that will be of public health benefit beyond COVID-19 in the years to come,” said Professor Angela Mathee.

Learn more about the SAMRC wastewater Surveillance Dashboard


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The GloPID-R Secretariat is a project which receives funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No 101094188.